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- EMDB-30887: Cryo-EM structure of amyloid fibril formed by familial prion dise... -

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Basic information

Entry
Database: EMDB / ID: EMD-30887
TitleCryo-EM structure of amyloid fibril formed by familial prion disease-related mutation E196K
Map dataMasked density map
Sample
  • Organelle or cellular component: Human prion E196K mutation amyloid fibril
    • Protein or peptide: Major prion protein
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive regulation of glutamate receptor signaling pathway / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding ...negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / positive regulation of glutamate receptor signaling pathway / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / cupric ion binding / negative regulation of dendritic spine maintenance / regulation of potassium ion transmembrane transport / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / long-term memory / response to cadmium ion / cellular response to copper ion / inclusion body / neuron projection maintenance / tubulin binding / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / protein-folding chaperone binding / amyloid-beta binding / protease binding / microtubule binding / nuclear membrane / molecular adaptor activity / response to oxidative stress / transmembrane transporter binding / learning or memory / postsynapse / regulation of cell cycle / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / negative regulation of apoptotic process / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsWang LQ / Zhao K
CitationJournal: Sci Adv / Year: 2021
Title: Genetic prion disease-related mutation E196K displays a novel amyloid fibril structure revealed by cryo-EM.
Authors: Li-Qiang Wang / Kun Zhao / Han-Ye Yuan / Xiang-Ning Li / Hai-Bin Dang / Yeyang Ma / Qiang Wang / Chen Wang / Yunpeng Sun / Jie Chen / Dan Li / Delin Zhang / Ping Yin / Cong Liu / Yi Liang /
Abstract: Prion diseases are caused by the conformational conversion of prion protein (PrP). Forty-two different mutations were identified in human PrP, leading to genetic prion diseases with distinct clinical ...Prion diseases are caused by the conformational conversion of prion protein (PrP). Forty-two different mutations were identified in human PrP, leading to genetic prion diseases with distinct clinical syndromes. Here, we report the cryo–electron microscopy structure of an amyloid fibril formed by full-length human PrP with E196K mutation, a genetic Creutzfeldt-Jakob disease–related mutation. This mutation disrupts key interactions in the wild-type PrP fibril, forming an amyloid fibril with a conformation distinct from the wild-type PrP fibril and hamster brain–derived prion fibril. The E196K fibril consists of two protofibrils. Each subunit forms five β strands stabilized by a disulfide bond and an unusual hydrophilic cavity stabilized by a salt bridge. Four pairs of amino acids from opposing subunits form four salt bridges to stabilize the zigzag interface of the two protofibrils. Our results provide structural evidences of the diverse prion strains and highlight the importance of familial mutations in inducing different strains.
History
DepositionJan 18, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00714
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.00714
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dwv
  • Surface level: 0.00714
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dwv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30887.png

Downloads & links

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Map

FileDownload / File: emd_30887.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 400 pix.
= 405.6 Å		1.01 Å/pix.
x 400 pix.
= 405.6 Å		1.01 Å/pix.
x 400 pix.
= 405.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00714 / Movie #1: 0.00714
Minimum - Maximum-0.011129221 - 0.027874239
Average (Standard dev.)0.000032199438 (±0.000523231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 405.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z405.600405.600405.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0110.0280.000

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Supplemental data

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Mask #1

Fileemd_30887_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked density map

Fileemd_30887_additional_1.map
AnnotationUnmasked density map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human prion E196K mutation amyloid fibril

EntireName: Human prion E196K mutation amyloid fibril
Components
  • Organelle or cellular component: Human prion E196K mutation amyloid fibril
    • Protein or peptide: Major prion protein

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Supramolecule #1: Human prion E196K mutation amyloid fibril

SupramoleculeName: Human prion E196K mutation amyloid fibril / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.996422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGGWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHSQWNK PSKPKTNMK HMAGAAAAGA VVGGLGGYML GSAMSRPIIH FGSDYEDRYY RENMHRYPNQ VYYRPMDEYS NQNNFVHDCV N ITIKQHTV ...String:
MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGGWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHSQWNK PSKPKTNMK HMAGAAAAGA VVGGLGGYML GSAMSRPIIH FGSDYEDRYY RENMHRYPNQ VYYRPMDEYS NQNNFVHDCV N ITIKQHTV TTTTKGKNFT ETDVKMMERV VEQMCITQYE RESQAYYQRG SS

UniProtKB: Major prion protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.40873 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.657 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24083
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6lni

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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